Internal e-mails from chemists and supervisors at a troubled state drug laboratory ­describe a staff drowning in work, instances of misplaced evidence in crime cases, and mounting frustrations over the Patrick administration’s seeming indifference.

“The situation in the evidence office is past the breaking point,” reads a Sept. 11, 2008, ­e-mail to Julianne Nassif, director of analytical chemistry at the Jamaica Plain lab, from an employee whose name was blacked out by the source of the documents. The documents were obtained Friday by the Globe from a source with direct knowledge of the lab’s operations.

Nassif was fired Wednesday, and a top official at the lab ­resigned, in a widening scandal over mishandled drug samples in a lab run until July by the ­Department of Public Health. Officials fear that the mis­handling may have affected thousands of cases over the past nine years, raising the specter of unwarranted convictions, ­errant deportations, and the wrongful taking of property.

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The 2008 e-mail describes one instance of drug samples mistakenly placed in an outgoing bin without being analyzed, and another in which staff spent hours looking for a sample that finally turned up in a different division’s office.

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The documents span 5½ years, from October 2006 through March of this year, when Annie Dookhan, a chemist at the center of the lab scandal, resigned. Investigators have provided few details about Dookhan’s alleged wrongdoing, but said she has admitted to some malfeasance involving mishandling drug evidence.

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The e-mails repeatedly ­recount pleas from district ­attorneys to lab workers to ­expedite cases, amid a growing backlog estimated in a March 5, 2012 e-mail as being at least nine months long.

In a Sept. 4, 2008, e-mail, Nassif writes to an unidentified lab employee that she understands the worker’s frustration and that she had scheduled a meeting with “the Commissioner” and “Undersecretary Grossman” later that month to discuss the issues. While Nassif did not use their full names, she is apparently referring to state Public Health Commissioner John Auerbach, whose agency ran the drug lab until State ­Police assumed control this summer, and former undersecretary of public safety John Grossman. What, if any, solutions were discussed in that meeting remains unclear, but an e-mail a few weeks later to Nassif from an employee warns that staff shortages and lack of space to store evidence had ­become “desperate.”

“It is very discouraging,” the note concludes, “to watch the situation get worse month by month and hear of no plans to improve things.”

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Department of Public Health spokesman David Kibbe said in a statement Friday that it was clear that “lab management failed and that’s why we took the administrative actions we did this week,” referring to Nassif’s firing and the resignation of her boss. “The investigation has been turned over to State Police, and these e-mails are part of that investigation looking into what happened at the drug lab,” Kibbe said.

Defense attorneys briefed by the Patrick administration on the lab scandal said that Dookhan, the chemist, allegedly ignored safeguards designed to ensure fair trials in drug cases and tampered with evidence in ways that may force dismissal of thousands of cases in Eastern Massachusetts.

In a letter to members of the Massachusetts Association of Criminal Defense Attorneys, association president Max D. Stern said his group along with federal and state public defenders
were given insights into why the State Police have notified prosecutors that 60,000 drug samples, representing 34,000 criminal cases, may now be tainted.

“The lab analyst in question had unsupervised access to the drug safe and evidence room, and tampered with evidence bags, altered the actual weight of the drugs, did not calibrate machines correctly, and altered samples so that they would test as drugs when they were not,’’ Stern wrote.

Terrel Harris, spokesman for the Executive Office of Public Safety and Security, confirmed that Dookhan had “unsupervised access to the evidence lockup.”

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Prosecutors in drug cases must be able to prove that substances seized by police are scientifically determined to be ­illicit drugs and have not been tampered with during the months, and often years, that pass between arrest and trial.

Seized drugs were taken by police to the Jamaica Plain lab, where they were supposed to be kept in a safe and signed out by chemists for testing. Afterward, the drugs were shipped back to police departments.

The impact of the scandal was highlighted Friday in ­Norfolk Superior Court, where Judge Mitchell Kaplan declined to rule on a request for freedom by David A. Danielli, who pleaded guilty this year to possessing 500 oxycodone pills. The evidence in Danielli’s case was tested in 2011 by Dookhan. Danielli’s case is among 90 ­Norfolk cases considered among the first wave of tainted prosecutions. The judge said his refusal was procedural and not based on the merits. He said Danielli, whose request for freedom has the support of Norfolk prosecutors, must go before the judge who accepted the guilty plea.

Kaplan’s ruling disappointed Danielli, who was sent back to the Norfolk House of Correction to serve more of his three-year sentence. “It was heartbreaking to see him sitting there,’’ said his daughter, Kristen Danielli. “I believe my dad was put in a position where he felt he needed to make that ­decision [to plead guilty] for the benefit of his family.’’

Defense attorney John T. Martin said he would file ­papers in Suffolk Superior Court, where the judge who heard the case now sits, and ask that jurist to quickly grant ­Danielli a hearing. Martin ­applauded Norfolk District ­Attorney Michael Morrissey’s office for supporting the request.

Dookhan worked in the lab from 2003 until her March resignation. As the State Police agency was assuming control of the lab in the summer, staff members there alerted police officials to concerns about Dookhan’s work.

On Thursday, top Patrick administration officials said that lab director Dr. Linda L. Han had resigned and ­Nassif had been fired. Disciplinary proceedings are underway against Dookhan’s direct super­visor.

Administration officials said Dookhan’s supervisors missed obvious signs of problems. In 2004, for example, Dookhan processed 9,239 samples while her peers tested an average of only 2,938 samples.

Executives at the lab discovered a problem with Dookhan in June 2011, but waited six months to tell their bosses at Department of Public Health headquarters. State officials have set up a “boiler room” of prosecutors, defense attorneys, court officials, and others to ­review the thousands of cases that might be affected.

Norfolk prosecutors were joined by Plymouth and Suffolk prosecutors in asking that bail be cut or eliminated in cases in which they have confirmed that Dookhan had a role.

Two cases handled by Suffolk District Attorney Daniel F. Conley’s office illustrate the complexity. Conley asked this week that ­Edward Dancy’s bail be cut from $30,000 cash to personal recognizance on charges he sold drugs to an undercover Boston police officer in 2010. But Conley’s office balked at cutting bail for ­Marcus Pixley, arrested on charges of selling drugs in the South End last year but also charged with resisting arrest. Pixley was previously convicted of rape and other charges, prosecutors said.

“What happened at the Department of Public Health lab was a catastrophic failure and there’s no simple, easy, or one-size-fits-all solution,’’ Conley said in a statement. “If someone is held or convicted on tainted evidence, we won’t hesitate to take every appropriate step to bring the case to light and correct the record. But if there are credible facts and evidence to support the legitimacy of an implicated case, we’ll work just as hard to ensure that the defendant is held accountable.”